Diversity of AMPA Receptor Ligands: Chemotypes, Binding Modes, Mechanisms of Action, and Therapeutic Effects
Abstract
:1. Introduction
2. AMPA Receptor Architecture and Mechanism of Operation
- Transmembrane AMPA receptor regulatory proteins (TARP), including the first discovered stargazine (γ2), γ3, γ4, γ5, γ7, and γ8. Their structure includes four transmembrane helices and a number of extracellular loops containing β-sheet fragments and disordered regions. The formation of complexes with TARP potentiates the AMPA receptor currents;
- Germ cell-specific gene 1-like protein (GSG1L) is similar to TARP in overall structure (allowing one to assign these two groups to the claudin family) but has an “inhibitory” effect on the receptor;
- Cornichon homolog (CNIH) proteins contain four transmembrane helices, with the spatial structure of their transmembrane domain being very similar to that of TARP (despite the different helix arrangement), but do not contain an extracellular domain;
- Cysteine-knot AMPA receptor modulating proteins (Shisa/CKAMP family) include one transmembrane domain, an extracellular cysteine-knot motif, and a long intracellular C-terminal tail;
- The SynDIG1 and SynDIG4 proteins (Dispanin C family) contain a single transmembrane domain and a long extracellular C-terminal tail with a membrane-associated domain.
3. Binding Sites and Ligand Types of the AMPA Receptor
- (1).
- The orthosteric binding site for agonists and competitive antagonists is located inside the clamshell of the ligand-binding domain;
- (2).
- The positive allosteric modulator binding site is located at the interface between the subunits of the dimeric ligand-binding domain;
- (3).
- The binding site for negative allosteric modulators (non-competitive antagonists, non-competitive inhibitors) is located in the linker region between the ligand-binding and transmembrane domains;
- (4).
- The binding site for TARP-dependent allosteric modulators is located at the interface between the interacting transmembrane segments of TARP and the receptor;
- (5).
- Ion channel blocker binding sites are located in the pore of the ion channel (mainly for the Ca2+-permeable forms of the receptor);
- (6).
- Con-ikot-ikot, a protein toxin from the Conus striatus cone snail, acts as an AMPAR positive allosteric modulator by binding on top of the LBD dimer-of-dimers (in the free space between LBDs and ATDs). This effectively immobilizes the LBD layer of the receptor and prevents desensitization, leading to prolonged receptor activation (although mostly to only partially open states), over-excitation, and toxicity [3,43]. It is not yet clear if this binding site could be exploited by the small molecule ligands.
- (7).
- Based on molecular modeling and structural data, another potential binding site is predicted to be located at the interface between the lower lobes of the subunits of the dimeric amino-terminal domain [44]. Presumably, this site is present (or druggable) only in the GluA3 receptors, while the ligands interacting with it are not known yet. Its position at the dimer interface is similar to that of the binding sites in related NMDA receptors, as well as in metabotropic glutamate receptors. Taking into account the specificity of the amino acid sequence of the AMPA receptor amino-terminal domain, these data make it a promising potential target for the development of new modulators with high selectivity.
- (8).
- Based on the analysis of the structure of the AMPA receptor complex with trans-4-butylcyclohexane carboxylic acid (4-BCCA), new binding sites were found in the transmembrane domain. Driven by the structural data as well as site-directed mutagenesis and molecular modeling, three possible mechanisms of action of 4-BCCA were proposed that involve either direct blocking of the ion channel (interfering with the flow of permeant ions), or influencing the dynamics of the M3 helices, or destabilizing the protein surface through competition with the surrounding membrane lipids [45]. Presumably, other related compounds which are inhibitors of the AMPA receptor also bind at these sites and can serve as promising potential antiepileptic drugs. Moreover, these sites are located in close proximity to those for the negative allosteric modulators, which opens the possibility of interaction of the respective structural fragments and could explain the synergistic effect observed with the simultaneous administration of perampanel and decanoic acid [46].
3.1. The Orthosteric Binding Site for Agonists and Competitive Antagonists
3.2. The Positive Allosteric Modulator (PAM) Binding Site
3.3. Binding Site for Negative Allosteric Modulators (Non-competitive Antagonists, Non-competitive Inhibitors)
3.4. Chemotypes with Activity Cliffs
3.5. Binding Site for TARP-Dependent Allosteric Modulators
3.6. Binding Sites for Ion Channel Blockers
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Golubeva, E.A.; Lavrov, M.I.; Radchenko, E.V.; Palyulin, V.A. Diversity of AMPA Receptor Ligands: Chemotypes, Binding Modes, Mechanisms of Action, and Therapeutic Effects. Biomolecules 2023, 13, 56. https://doi.org/10.3390/biom13010056
Golubeva EA, Lavrov MI, Radchenko EV, Palyulin VA. Diversity of AMPA Receptor Ligands: Chemotypes, Binding Modes, Mechanisms of Action, and Therapeutic Effects. Biomolecules. 2023; 13(1):56. https://doi.org/10.3390/biom13010056
Chicago/Turabian StyleGolubeva, Elena A., Mstislav I. Lavrov, Eugene V. Radchenko, and Vladimir A. Palyulin. 2023. "Diversity of AMPA Receptor Ligands: Chemotypes, Binding Modes, Mechanisms of Action, and Therapeutic Effects" Biomolecules 13, no. 1: 56. https://doi.org/10.3390/biom13010056
APA StyleGolubeva, E. A., Lavrov, M. I., Radchenko, E. V., & Palyulin, V. A. (2023). Diversity of AMPA Receptor Ligands: Chemotypes, Binding Modes, Mechanisms of Action, and Therapeutic Effects. Biomolecules, 13(1), 56. https://doi.org/10.3390/biom13010056